Deoxyribonucleic acid (DNA) sequencing is the process of determining the precise order of nucleotides within a DNA molecule, e.g., the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA. Knowledge of DNA sequences has become useful for basic biological research, and in numerous applied fields such as diagnostic, biotechnology, forensic biology, and biological systematics. The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbial species. The advent of these rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Sequencing by hybridization (SBH) is a method of sequencing based on hybridization, or lack thereof, of a large number of different probe sequences to a target nucleic acid. By detecting hybridization of overlapping probes and absence of hybridization of probes of similar but different sequence, one can predict the nucleotide sequence of a target sequence.
However, due to noise, errors, or other imperfections in a sequencing system, the detected hybridization signals, when mapped to a dye space for assay calling, may be overlapped and densely packed, and thus are difficult to distinguish from each other for the correct identification of which probes hybridize with a given target nucleic acid.